Iron in PDB 8w79: Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin

The structure of Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin, PDB code: 8w79 was solved by W.M.Wang, H.F.Xi, W.J.Gong, D.Y.Ma, H.F.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.83 / 2.70
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.406, 180.406, 180.406, 90, 90, 90
R / Rfree (%)	19.3 / 25.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Iron atom in the Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin (pdb code 8w79). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 11 binding sites of Iron where determined in the Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin, PDB code: 8w79:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 11 in the Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:70.3 occ:1.00 OD1 A:ASP138 1.8 78.2 1.0 OD2 A:ASP142 2.0 71.2 1.0 OD2 A:ASP60 2.1 79.3 1.0 NE2 A:HIS65 2.4 62.3 1.0 CG A:ASP142 2.8 70.2 1.0 OD1 A:ASP142 3.0 75.5 1.0 CG A:ASP138 3.1 70.7 1.0 CE1 A:HIS65 3.2 57.6 1.0 NZ A:LYS141 3.3 87.5 1.0 CG A:ASP60 3.4 63.4 1.0 CD2 A:HIS65 3.5 60.5 1.0 OD2 A:ASP138 3.8 88.7 1.0 OD1 A:ASP60 4.1 84.4 1.0 CB A:ASP138 4.1 62.8 1.0 CB A:ASP142 4.2 58.3 1.0 ND1 A:HIS65 4.4 60.0 1.0 CB A:ASP60 4.4 48.4 1.0 O A:ASP138 4.5 67.8 1.0 CG A:HIS65 4.6 67.3 1.0 NZ A:LYS61 4.6 69.6 1.0 CE A:LYS141 4.6 91.4 1.0 CH2 A:TRP134 4.7 57.7 1.0 CE A:LYS61 4.7 59.8 1.0

Iron binding site 2 out of 11 in the Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:137.2 occ:0.25 OE1 A:GLU164 2.2 119.0 1.0 O A:HOH306 2.2 113.0 0.2 FE A:FE205 2.5 132.2 0.2 O A:HOH301 3.1 102.7 1.0 CD A:GLU164 3.2 107.3 1.0 OE2 A:GLU164 3.6 99.1 1.0 FE A:FE210 4.2 158.0 1.0 CG A:GLU164 4.5 77.7 1.0

Iron binding site 3 out of 11 in the Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:175.2 occ:1.00 FE A:FE204 2.6 171.1 1.0 OE1 A:GLU168 2.6 120.2 1.0 O A:HOH307 2.8 91.9 1.0 O A:HOH308 3.0 115.5 1.0 O A:HOH313 3.3 123.2 1.0 CD A:GLU168 3.8 115.1 1.0 OE2 A:GLU171 4.0 104.0 1.0 O A:HOH315 4.3 110.7 0.2 FE A:FE210 4.5 158.0 1.0 OE2 A:GLU168 4.6 120.0 1.0 CG A:GLU168 4.8 87.7 1.0 O A:HOH312 4.8 30.0 0.2 CD A:GLU171 4.9 115.7 1.0

Iron binding site 4 out of 11 in the Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe204 b:171.1 occ:1.00 O A:HOH312 2.5 30.0 0.2 FE A:FE203 2.6 175.2 1.0 O A:HOH315 2.6 110.7 0.2 FE A:FE210 2.9 158.0 1.0 O A:HOH313 3.1 123.2 1.0 OE1 A:GLU168 3.4 120.2 1.0 O A:HOH308 4.0 115.5 1.0 O A:HOH307 4.1 91.9 1.0 CD A:GLU168 4.4 115.1 1.0 OE2 A:GLU168 4.6 120.0 1.0 O A:HOH306 4.7 113.0 0.2

Iron binding site 5 out of 11 in the Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe205 b:132.2 occ:0.25 FE A:FE202 2.5 137.2 0.2 OE2 A:GLU164 2.9 99.1 1.0 OE1 A:GLU164 3.1 119.0 1.0 CD A:GLU164 3.4 107.3 1.0 O A:HOH306 4.8 113.0 0.2 CG A:GLU164 4.8 77.7 1.0 CD1 A:ILE161 4.9 49.6 1.0 O A:HOH301 4.9 102.7 1.0

Iron binding site 6 out of 11 in the Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe206 b:145.0 occ:1.00 O A:HOH311 2.3 73.3 1.0 OE2 A:GLU145 3.7 91.7 1.0 NZ A:LYS141 3.9 87.5 1.0 OE1 A:GLU145 4.0 71.7 1.0 OD1 A:ASP142 4.2 75.5 1.0 CD A:GLU145 4.3 89.0 1.0 OD2 A:ASP60 4.6 79.3 1.0 CG A:ASP60 4.7 63.4 1.0 CD A:LYS141 4.8 74.0 1.0 OD1 A:ASP60 4.8 84.4 1.0 CE A:LYS141 4.9 91.4 1.0

Iron binding site 7 out of 11 in the Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe207 b:95.8 occ:1.00 ND1 A:HIS23 3.1 46.9 1.0 CB A:HIS112 3.3 44.3 1.0 CG A:HIS112 3.5 60.6 1.0 CA A:HIS23 3.6 40.3 1.0 N A:HIS23 3.8 45.4 1.0 CD1 A:LEU26 3.8 46.8 1.0 CB A:HIS23 3.9 36.5 1.0 CG A:GLN22 3.9 69.7 1.0 CG A:HIS23 3.9 32.9 1.0 CD2 A:HIS112 4.0 70.4 1.0 ND1 A:HIS112 4.0 69.5 1.0 C A:GLN22 4.1 47.9 1.0 CE1 A:HIS23 4.1 47.8 1.0 O A:GLN22 4.2 44.7 1.0 O A:ALA19 4.5 48.0 1.0 CB A:GLN22 4.5 36.4 1.0 CB A:LEU26 4.5 39.3 1.0 CA A:HIS112 4.6 45.1 1.0 NE2 A:HIS112 4.6 59.6 1.0 CE1 A:HIS112 4.7 62.5 1.0 NE2 A:GLN22 4.8 63.9 1.0 CD1 A:ILE116 4.8 37.8 1.0 CG A:LEU26 4.9 45.2 1.0 CA A:GLN22 4.9 48.1 1.0 CD A:GLN22 5.0 98.8 1.0 C A:HIS23 5.0 42.5 1.0

Iron binding site 8 out of 11 in the Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe208 b:109.1 occ:1.00 OD1 A:ASP124 3.7 56.4 1.0 OD2 A:ASP124 3.8 62.3 1.0 CG A:ASP124 4.2 51.9 1.0 O A:LEU121 4.4 54.2 1.0 O A:ALA122 5.0 51.4 1.0

Iron binding site 9 out of 11 in the Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe209 b:148.4 occ:0.25 O A:HOH316 2.7 82.1 1.0 O A:HOH315 3.7 110.7 0.2 O A:HOH313 3.9 123.2 1.0

Iron binding site 10 out of 11 in the Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Fe-O Nanocluster of Form-III in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe210 b:158.0 occ:1.00 O A:HOH306 2.7 113.0 0.2 FE A:FE204 2.9 171.1 1.0 O A:HOH312 2.9 30.0 0.2 OE1 A:GLU168 3.2 120.2 1.0 OE2 A:GLU168 3.3 120.0 1.0 CD A:GLU168 3.5 115.1 1.0 FE A:FE202 4.2 137.2 0.2 O A:HOH301 4.4 102.7 1.0 FE A:FE203 4.5 175.2 1.0 OE1 A:GLU164 4.5 119.0 1.0 CG A:GLU168 4.7 87.7 1.0 O A:HOH315 4.9 110.7 0.2

W.Wang, H.Xi, D.Fu, D.Ma, W.Gong, Y.Zhao, X.Li, L.Wu, Y.Guo, G.Zhao, H.Wang. Growth Process of Fe-O Nanoclusters with Different Sizes Biosynthesized By Protein Nanocages. J.Am.Chem.Soc. V. 146 11657 2024.
ISSN: ESSN 1520-5126
PubMed: 38641862
DOI: 10.1021/JACS.3C13830